[MINC-users] MNI tools in Freesurfer

[Fornito, Alexander]

Hi,
We seem to have got it working now, thanks!
However, when Freesurfer calls nu_correct, I get the following message:

nu_correct -clobber nu/nu0.mnc nu/nu1.mnc
[alex@flanders:/data/flanders/work/alex/freesurfer/subjects/186_good/mri/] [2005-06-07 12:04:01] running:
  /usr/local/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /var/tmp/nu_correct_14595/ nu/nu0.mnc nu/nu1.imp

Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Processing:.................................................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Processing:.................................................................Done

...and so on, for quite some time, before moving on to other processes. Is the 

Not implemented yet in cache_volume_range_has_changed() message indicative of some kind of error?
Thanks for your help,
Alex

-----Original Message-----
From:	Andrew Janke [mailto:a.janke@gmail.com]
Sent:	Thu 6/2/2005 7:15 PM
To:	minc-users@bic.mni.mcgill.ca
Cc:	
Subject:	Re: [MINC-users] MNI tools in Freesurfer
Wierd, I had thought all the packages from now on were using static
libraries.  Anyhow, I presume you got the .deb packages from
packages.bic.mni.mcgill.ca/deb?

If so, then I'd still like to know why they are using shared libraries
but the fix is to simply add:

   /usr/local/mni/lib to your LD_LIBRARY_PATH

andrew

On 01/06/05, Fornito, Alexander <Alexander.Fornito@wh.org.au> wrote:
> Hi all,
> I've been having trouble with the MNI tools packaged together with Freesurfer. We are running a  linux kernel 2.4.26 debian 3.0 (woody).
> We've installed the freesurfer and the packaged MNI tools in the apporpriate directories and set the appropriate environment variables.
> When I run Freesurfer's segmentation algorithm, I get the following error messages:
> 
> segment_subject 190
> cp: cannot stat
> `/data/flanders/work/alex/freesurfer/subjects/scripts/brain.dat'
> : No such file or directory
> /data/flanders/work/alex/freesurfer/subjects/190/scripts
> /data/flanders/work/ale
> x/freesurfer/subjects
> registering 190
> mri_convert orig orig/orig.mnc
> reading from orig...
> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-1, 0, 0)
> j_ras = (0, 0, -1)
> k_ras = (0, 1, 0)
> writing to orig/orig.mnc...
> mincinfo: error while loading shared libraries: libvolume_io.so.0:
> cannot open shared object file: No such file or directory
> Error executing mincinfo on orig/orig.mnc
> Error:  could not open file
> "/data/flanders/work/alex/freesurfer/subjects/190/mr
> i/transforms/talairach.xfm".
> System message: No such file or directory
> mri_add_xform_to_header: could not read xform file
> '/data/flanders/work/alex/fre
> esurfer/subjects/190/mri/transforms/talairach.xfm'
> 
> On their own some of the MNI tools work (eg., Display), whereas others don't (eg., mritotal, which returns with the mincinfo: error while loading shared libraries: libvolume_io.so.0 message).
> Any help would be greatly appreciated!!!
> Thanks,
> Alex
> 
> _______________________________________________
> MINC-users@bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> 


-- 
Andrew Janke      (a.janke@gmail.com || www.cmr.uq.edu.au/~rotor)
Australia->Brisbane     H: +61 7 3390 6332  || M: +61 4 2138 8581

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